Download GATK version 1.4

etheringethering Posts: 1Member
edited January 2013 in Ask the GATK team

Hi,
I want to run GATK in Galaxy and the required version is 1.4.
Can you tell me where I can download this from? I've got the source for version 1.4 from github, so I can build it if need be, but I was wondering if there's a repository for older binaries.
Many thanks,
Graham

Post edited by Geraldine_VdAuwera on

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,973Administrator, GATK Developer admin

    Hi Graham,
    No, we don't provide older binaries, you'll need to compile your own.
    Note that we strongly recommend using more recent versions, as older versions have bugs that have been fixed in the newer...
    Good luck!

    Geraldine Van der Auwera, PhD

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,973Administrator, GATK Developer admin

    Oops, correction -- we do have the old binaries, they're on our public FTP server.

    Geraldine Van der Auwera, PhD

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,973Administrator, GATK Developer admin

    And another correction -- they're in a private dir on the ftp, so I've copied the most relevant ones to our public dropbox here:
    https://www.dropbox.com/sh/1misjysdehceq4h/GnQB948vMl

    Geraldine Van der Auwera, PhD

  • jorges1000jorges1000 Posts: 1Member

    I tried version 1.6-13-g91f02df in Galaxy and it works fine, at least for the tools I have tested.

  • TgongTgong Posts: 2Member

    Can I get the GATK version 2.0 but before 2.4? I want to use the somaticindeldetector. Thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,973Administrator, GATK Developer admin

    Hi @Tgong,

    We're not hosting the binaries, but if you want you can download the source code and build whichever version you want. See the Downloads page for access to the code repository.

    Geraldine Van der Auwera, PhD

  • arkalarkal Posts: 1Member

    so i have NO idea t all how to get the binary for gatk 2.3.9 from the source code....sigh the inconvenience of not being familiar with java... anyway.... can anyone help me out here and post the binary for 2.3.9? i need t use somatic indel detector

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,973Administrator, GATK Developer admin
    edited May 2013

    Hi @arkal,

    It's actually really easy to build from source, you should give it a try -- you will feel empowered for future work!

    1. Get the package for the version you want from this page: https://github.com/broadgsa/gatk-protected/tags

    2. From your terminal/console, navigate to the directory containing the source code. There, you run the command:

      ant clean dist

    This will do everything for you. The compiled binary will be in the newly-created dist directory.

    Post edited by Geraldine_VdAuwera on

    Geraldine Van der Auwera, PhD

  • stechenstechen University of PennsylvaniaPosts: 23Member

    Greetings!

    I tried doing this for GATK v2.2 and the error message said "Buildfile: build.xml does not exist!" even though I see it in the directory. Am I missing something?

    Thanks!
    Stephanie

  • stechenstechen University of PennsylvaniaPosts: 23Member

    Sorry, nevermind, it works when one is logged into the node.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,973Administrator, GATK Developer admin

    Greetings, Stephanie, and glad it's working for you now :)

    Geraldine Van der Auwera, PhD

  • stechenstechen University of PennsylvaniaPosts: 23Member

    Thanks Geraldine!

    But I have another question. I'm running GATK v2.2 on whole genome data aligned to hg19. In the very first GATK step, the output log file has this in the header:

    "WARN 13:11:21,653 VCFStandardHeaderLines$Standards - Repairing standard header line for field AF because -- count types disagree; header has UNBOUNDED but standard is A -- descriptions disagree; header has 'Allele Frequency' but standard is 'Allele Frequency, for each ALT allele, in the same order as listed'
    INFO 13:11:21,657 RMDTrackBuilder - Loading Tribble index from disk for file /gpfs/fs121/h/stechen/reference_files/sorted_dbsnp_132.hg19.vcf "

    But it seems to still run. Is that okay?

    Thanks!
    Stephanie

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,973Administrator, GATK Developer admin

    Yes, it should be okay; your dbsnp file sounds like it's a bit out of spec, but GATK will have handled it properly.

    Geraldine Van der Auwera, PhD

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